In 3630 BBY the Eternal Fleet under control of Emperor Arcann attack the secret base of the Alliance that opposed him on the planet Odessen after learning its location from SCORPIO. During the Battle of Odessen the Alliance Commander defeated Arcann, who was taken by his mother Senya Tirall to recuperate, allowing his sister Vaylin to claim the Eternal Throne. Arcann was later redeemed by his mother on Voss and joined the Alliance alongside his mother to put an end to his sister's reign of terror. For a time, Vaylin was hindered by a mental conditioning imposed on her by Valkorion, but after she managed to get rid of it on Nathema, she immediately ordered the Eternal Fleet to attack Odessen again, intending to finish the Alliance for good.
The attack came at the unfortunate moment for the Alliance, as the Gravestone, their most valuable asset and the only ship powerful enough to stand against the Eternal Fleet, was caught in the dry dock, while the upgrades based on schematics obtained on Iokath were being installed. The Alliance fleet met Vaylin's forces in Odessen's orbit, but without the Gravestone was unable to prevent Zakuulan ground forces from landing. In almost two years that Alliance have operated on the planet, they erected formidable defenses around their base, including a planetary shield that protected the entire surrounding area from orbital bombardment and aerial attack. Former Republic Admiral Bey'wan Aygo took charge of Odessen's defense and made an urgent call to the Alliance Commander, Theron Shan and Lana Beniko, who were away from the base on a mission to Nathema, informing them of the attack and urging them to rush back as soon as possible. The Eternal Empire send a massive number of troops and ground vehicles to the surface of Odessen, with World thrashers clearing landing spots in Odessen wilderness, Zakuul Hovercrafts deploying battalions of troops and Eternal Empire Walkers providing heavy firepower for the ground forces.
The initial wave of Zakuulan troops focused on taking the Gravestone, which would instantly negate any advantage the Alliance had, but Captain Koth Vortena's crew sealed all entrances and frantically worked on finishing the upgrades to get the ship airborne. Around the Alliance base and in untamed Odessen wilderness, the Alliance had shown strong resistance as well, although Vaylin's forces still had superior numbers. Heavy fighting broke all around the base, with former Republic and Imperial soldiers as well as high-profile Alliance recruits fighting side by side against the Eternal Empire forces. Qyzen Fess joined with the Trandoshan Warstalkers, while Torian Cadera led a group of Mandalorians to reinforce Bey'wan Aygo's position. Voss Mystic Sana-Rae and her Force-sensitive students attempted to defend the Gravestone, but were forced to retreat when the enemy deployed heavy artillery around it. Vette volunteered to take care of the artillery guns with a rocket launcher provided to her by Doctor Juvard Illip Oggurobb, who himself was busy securing the research inside his base.
The shuttle carrying the Alliance Commander, Theron Shan and Lana Beniko arrived when the battle was already in full swing, and Theron dropped off Lana and the Commander in a safe spot not far from the base, while he himself decided to sneak behind the enemy lines and wreak havoc there. To made their path through the battle to the besieged Gravestone, the Commander and Lana commandeered an Eternal Empire Walker from the Vaylin's forces, using its firepower to destroy the enemy communication arrays and clear themselves a direct path to the Gravestone. By then enemy troops have broken through the Alliance lines and started cutting their way through the Gravestone hull, attempting to get inside. Vaylin's brother and redeemed former Emperor Arcann and his mother Senya Tirall arrived to aid in its defense, giving enough time for the Commander and Lana to join them and defeat the Knight Tyrral Jerikko who led the assault. A large group of Zakuulan Walkers then threatened to overwhelm their position, but Vortena and his crew have finished installing the upgrades just in time to activate the ship's cannons and destroy the walkers, after which the Gravestone took off into space to face the Eternal Fleet. However, even that was not enough to turn the tide of the battle, and the Commander decided to lure Vaylin away from the safety of her flagship and down to the surface for a personal confrontation. Lana went to join Theron, while Senya and Arcann offered to stand by the Commander's side against Vaylin. With the dry dock no longer the central focus of the battle, Sana-Rae led the Force-users in a counter-attack against the enemy flank, while the Commander went to look for a way to contact Vaylin as enemy reinforcements assaulted Aygo's line of defence from the west.
Having defeated Imperator Sunfell, the Commander used her holocomm to call Vaylin, successfully taunting her into a face-to-face confrontation. The Commander, Senya and Arcann commandeered another walker to clear out as many troops as possible before Vaylin's arrival, defeating a Siege Skytrooper before disembarking and requesting status updates. By this point Torian was the only one left from this unit, who were cut off by enemy ambush, which now threatened to overrun his position. At the same time Vaylin's forces have pinned down Vette on another end of the battlefield, her position given away when she destroyed the artillery guns. The Commander made a tough decision to save one of their allies first, reaching their position just in time to clear off enemy forces that surrounded them. Along with Senya and Arcann, the Commander then rushed to aid the other combatant, but Vaylin had gotten to them first, taking her victim prisoner and sending to Commander the coordinates for a direct confrontation on the Alliance landing platform. The Commander, Senya and Arcann rushed back to the Alliance base, where Oggurobb's position was being overrun while Gault and Bowdaar have barricaded themselves inside the Alliance headquarters. Southern perimeter of Aygo's defence had been breached by enemy forces, who also pushed back Sana-Rae and her students, requiring Aygo to send reinforcements their way. The Commander, Senya and Arcan approached the Alliance base from the hangar entrance, where Aric Jorgan assisted them from a sniper vantage point, and having cleared the base of enemies, proceeded to the face-to-face with Vaylin.
Vaylin was waiting for her family with a host of skytroopers and Horizon Guards at her side, and the prisoner at her mercy. After Valkorion appeared in front of his daughter, calling Vaylin not worthy of the Eternal Throne and not fit to rule the Eternal Empire, she responded by throwing her hostage at the Commander in a gesture of contempt, while reaching out with the Force to snap her victim's neck at the same time. This shocked Senya and Arcann, who stood at Commander's side in this confontation, agreeing that there was no other choice but to permanently stop Vaylin, who engaged her entire family with her full unleashed power. The Commander bested her in lightsaber combat, but Vaylin unleashed a massive Force Storm with her power, threatening to bring down the entire Alliance base. Having no other way to stop her, the Commander was forced to strike Vaylin down, ending her life. Aygo then reported that Eternal Empire soldiers began surrendering by the thousands and Koth confirmed that the Eternal Fleet had retreated, with Arcann theorizing that his sister's rage was only thing giving her troops as will to fight.
Gathering in the war room in the aftermath of their victory, the Alliance lamented the losses taken during the battle, while Arcann warned the Commander about a strange flow of energy he felt right after his sister's death, and warned them to beware Valkorion's machinations. However before anyone could get rest, Aygo received emergency calls from Sith Empress Darth Acina about the Eternal Fleet warships bombarding Dromund Kaas, as well as Coruscant and the other Core Worlds. Valkorion explained that with the Eternal Throne empty, the fleet's GEMINI captains have gone rogue, reverting the Fleet to its original function of exterminating all complex life in the galaxy. With claiming the Eternal Throne as the only way to stop the destruction, the entire Alliance leadership boarded the Gravestone and departed for Zakuul, where they found the planet blockaded by the Eternal Fleet, engaging it in the Battle of Zakuul.
Several elements of the battle can play differently, depending on the player's choices. If the player previously killed or exiled Koth Vortena, Hylo Visz will take his place as the captain of the Gravestone, installing the Iokath updates and piloting the ship against the Eternal Fleet. If the player previously killed Arcann and Senya Tirall, Theron Shan will arrive to defend the Gravestone in their place, after which he will join Lana in accompanying the player to the confrontation with Vaylin instead of assaulting the enemy flank. An optional objective during the Chapter VIII: End Times requires the player to locate eight other Alliance members on the battlefield, of which only Gault Rennow is present no matter the choices, while the rest will be replaced with generic Alliance members if the player does have them as companions. Either Aric Jorgan or Kaliyo Djannis can be killed or exiled during Knights of the Fallen Empire Chapter XIII: Profit and Plunder, while the rest are recruits from optional Alliance alerts mission, which can be done independently of the main story in almost any order. Alerts for recruiting Yuun, Qyzen Fess and Bowdaar are available to all players, while the alert for Pierce is only available to Imperial-side players, and Nico Okarr is only available to players who were subscribed on August 10, 2015. When the player is presented with the choice to save either Vette or Torian Cadera, neither option is a Light or a Dark side choice. Player has to choose which companion to save, while the other one will be captured and later killed by Vaylin.